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Nucleic Acids Research 2006 34(Web Server issue):W116-W118; doi:10.1093/nar/gkl282
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz and Jie Liang*

Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago Chicago, IL 60612, USA

*To whom correspondence should be addressed. Tel: +1 312 355 1789; Fax: +1 312 413 2 18; Email: jliang{at}uic.edu

Received February 9, 2006. Revised March 4, 2006. Accepted April 5, 2006.

Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp (http://cast.engr.uic.edu) is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease. These annotated residues are mapped to surface pockets, interior voids or other regions of the PDB structures. We use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB. The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.

Present addresses: Andrew Binkowski, Argonne National Laboratories, Argonne, IL 60439 USA

Yaron Turpaz, Affymetrix, Inc., Santa Clara, CA 95051, USA


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